Topological dynamics of an intrinsically disordered N-terminal domain of the human androgen receptor

Vahid Sheikhhassani, Barbara Scalvini, Julian Ng, Laurens W H J Heling, Yosri Ayache, Tom M J Evers, Eva Estébanez-Perpiñá, Iain J McEwan, Alireza Mashaghi

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Human androgen receptor contains a large N-terminal domain (AR-NTD) that is highly dynamic and this poses a major challenge for experimental and computational analysis to decipher its conformation. Misfolding of the AR-NTD is implicated in prostate cancer and Kennedy's disease, yet our knowledge of its structure is limited to primary sequence information of the chain and a few functionally important secondary structure motifs. Here, we employed an innovative combination of molecular dynamics simulations and circuit topology (CT) analysis to identify the tertiary structure of AR-NTD. We found that the AR-NTD adopts highly dynamic loopy conformations with two identifiable regions with distinct topological make-up and dynamics. This consists of a N-terminal region (NR, residues 1-224) and a C-terminal region (CR, residues 225-538), which carries a dense core. Topological mapping of the dynamics reveals a traceable time-scale dependent topological evolution. NR adopts different positioning with respect to the CR and forms a cleft that can partly enclose the hormone-bound ligand-binding domain (LBD) of the androgen receptor. Furthermore, our data suggest a model in which dynamic NR and CR compete for binding to the DNA-binding domain of the receptor, thereby regulating the accessibility of its DNA-binding site. Our approach allowed for the identification of a previously unknown regulatory binding site within the CR core, revealing the structural mechanisms of action of AR inhibitor EPI-001, and paving the way for other drug discovery applications.

Original languageEnglish
Article numbere4334
Number of pages17
JournalProtein science : a publication of the Protein Society
Issue number6
Early online date26 May 2022
Publication statusPublished - Jun 2022

Bibliographical note

We are thankful to Eugene Shakhnovich (Harvard University) for critical reading of the manuscript, and to Peter Bolhuis and Ioana Ilie (University of Amsterdam) for technical discussions. The research in Mashaghi lab is supported by funding from Muscular Dystrophy Association (USA), Grant Number MDA628071, and Dutch Research Council (Nederlandse Organisatie voor Wetenschappelijk Onderzoek) through NWA-IDG (NWA.1228.192.309) and Open Competition XS (OCENW.XS.076).


  • Androgen Receptor Antagonists/chemistry
  • DNA
  • Humans
  • Male
  • Prostatic Neoplasms/metabolism
  • Protein Domains
  • Receptors, Androgen/chemistry


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